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The World Health Organisation has called for global action to reduce child stunting by 40% by 2025. One third of the world's stunted children live in India, and children belonging to rural indigenous communities are the worst affected. We sought to identify the strongest determinants of stunting among indigenous children in rural Jharkhand and Odisha, India, to highlight key areas for intervention. We analysed data from 1227 children aged 6–23.99 months and their mothers, collected in 2010 from 18 clusters of villages with a high proportion of people from indigenous groups in three districts. We measured height and weight of mothers and children, and captured data on various basic, underlying and immediate determinants of undernutrition. We used Generalised Estimating Equations to identify individual determinants associated with children's height‐for‐age z‐score (HAZ; p < 0.10); we included these in a multivariable model to identify the strongest HAZ determinants using backwards stepwise methods. In the adjusted model, the strongest protective factors for linear growth included cooking outdoors rather than indoors (HAZ +0.66), birth spacing ≥24 months (HAZ +0.40), and handwashing with a cleansing agent (HAZ +0.32). The strongest risk factors were later birth order (HAZ −0.38) and repeated diarrhoeal infection (HAZ −0.23). Our results suggest multiple risk factors for linear growth faltering in indigenous communities in Jharkhand and Odisha. Interventions that could improve children's growth include reducing exposure to indoor air pollution, increasing access to family planning, reducing diarrhoeal infections, improving handwashing practices, increasing access to income and strengthening health and sanitation infrastructure. [ABSTRACT FROM AUTHOR]